Initialize at openlb-1-3

55 files changed, 9479 insertions, 0 deletions

diff --git a/src/io/MakeHeader b/src/io/MakeHeader
new file mode 100644
index 0000000..d86ae79
--- /dev/null
+++ b/src/io/MakeHeader
@@ -0,0 +1,48 @@
+#  This file is part of the OpenLB library
+#
+#  Copyright (C) 2007 Mathias Krause
+#  E-mail contact: info@openlb.net
+#  The most recent release of OpenLB can be downloaded at
+#  <http://www.openlb.net/>
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public
+#  License along with this program; if not, write to the Free
+#  Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+#  Boston, MA  02110-1301, USA.
+
+
+generic        := fileName \
+                  gnuplotWriter \
+                  ostreamManager \
+                  parallelIO \
+                  vtiReader \
+                  vtiWriter \
+                  xmlReader
+
+precompiled    :=  base64 \
+                   blockGifWriter \
+                   blockVtkWriter2D \
+                   blockVtkWriter3D \
+                   colormaps \
+                   fileName \
+                   gnuplotWriter \
+                   gnuplotHeatMapWriter \
+                   ostreamManager \
+                   parallelIO \
+                   serializerIO \
+                   stlReader \
+                   superVtmWriter2D \
+                   superVtmWriter3D \
+                   vtiReader \
+                   vtiWriter \
+                   xmlReader
diff --git a/src/io/base64.cpp b/src/io/base64.cpp
new file mode 100644
index 0000000..de373e0
--- /dev/null
+++ b/src/io/base64.cpp
@@ -0,0 +1,72 @@
+/*  This file is part of the OpenLB library
+ *
+ *  Copyright (C) 2007 Jonas Latt
+ *  E-mail contact: info@openlb.net
+ *  The most recent release of OpenLB can be downloaded at
+ *  <http://www.openlb.net/>
+ *
+ *  This program is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License
+ *  as published by the Free Software Foundation; either version 2
+ *  of the License, or (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public
+ *  License along with this program; if not, write to the Free
+ *  Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+ *  Boston, MA  02110-1301, USA.
+*/
+
+#include "base64.h"
+#include "base64.hh"
+
+namespace olb {
+
+// All of the following is a workaround to the following problem: on a
+// 32-bit machine where unsigned int is the same as size_t, Base64Encoder
+// needs to be instantiated on one integer type only. On some 64-bit
+// platforms however, size_t is not equal to unsigned int. In that case,
+// Base64Encoder needs to be instantiated twice. It is however not
+// possible to instantiate this class first on unsigned int and then
+// on size_t, because this yields a double instantiation, and thus
+// an error, where these types are the same. To avoid this problem,
+// the chosen instantiation types are unsigned int and size_t where
+// these types are different, and unsigned char and unsigned int where
+// they are similar. A template-based if-then-else construct is used
+// to distinguish the two cases.
+
+template<bool areEqual> struct DistinctUint;
+
+template<>
+struct DistinctUint<true> {
+  typedef unsigned char T1;
+  typedef size_t T2;
+};
+
+template<>
+struct DistinctUint<false> {
+  typedef unsigned int T1;
+  typedef size_t T2;
+};
+
+typedef DistinctUint<sizeof(unsigned int)==sizeof(size_t)>::T1 T1;
+typedef DistinctUint<sizeof(unsigned int)==sizeof(size_t)>::T2 T2;
+
+template class Base64Encoder<bool>;
+template class Base64Encoder<float>;
+template class Base64Encoder<double>;
+template class Base64Encoder<T1>;
+template class Base64Encoder<T2>;
+template class Base64Encoder<unsigned char>;
+
+template class Base64Decoder<bool>;
+template class Base64Decoder<float>;
+template class Base64Decoder<double>;
+template class Base64Decoder<T1>;
+template class Base64Decoder<T2>;
+
+}
diff --git a/src/io/base64.h b/src/io/base64.h
new file mode 100644
index 0000000..f2248e6
--- /dev/null
+++ b/src/io/base64.h
@@ -0,0 +1,82 @@
+/*  This file is part of the OpenLB library
+ *
+ *  Copyright (C) 2007 Jonas Latt
+ *  E-mail contact: info@openlb.net
+ *  The most recent release of OpenLB can be downloaded at
+ *  <http://www.openlb.net/>
+ *
+ *  This program is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License
+ *  as published by the Free Software Foundation; either version 2
+ *  of the License, or (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public
+ *  License along with this program; if not, write to the Free
+ *  Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+ *  Boston, MA  02110-1301, USA.
+*/
+
+/* Acknowledgment: The strategy adopted here to encode
+ * and decode Base64, and in particular the expression of the
+ * arrays Base64Encoder::enc64 and Base64Decoder::dec64,
+ * is inspired by the open source library b64 by Bob Trower,
+ * which is distributed with a MIT license at the address
+ * http://base64.sourceforge.net/b64.c
+ */
+
+
+#ifndef BASE64_H
+#define BASE64_H
+
+#include <iosfwd>
+
+namespace olb {
+
+template<typename T>
+class Base64Encoder {
+public:
+  Base64Encoder(std::ostream& ostr_, size_t fullLength_);
+  void encode(const T* data, size_t length);
+private:
+  void fillOverflow(const unsigned char* charData, size_t charLength, size_t& pos);
+  void flushOverflow();
+  void writeSize();
+  void encodeBlock( const unsigned char* data);
+  void encodeUnfinishedBlock( const unsigned char* data, int length);
+private:
+  static const char enc64[65];
+private:
+  std::ostream& ostr;
+  size_t charFullLength;
+  size_t numWritten;
+  int numOverflow;
+  unsigned char overflow[3];
+};
+
+template<typename T>
+class Base64Decoder {
+public:
+  Base64Decoder(std::istream& istr_, size_t fullLength_);
+  void decode(T* data, size_t length);
+private:
+  void flushOverflow(unsigned char* charData, size_t charLength, size_t& pos);
+  unsigned char getNext();
+  void decodeBlock(unsigned char* data);
+private:
+  static const char dec64[82];
+private:
+  std::istream& istr;
+  size_t charFullLength;
+  size_t numRead;
+  int posOverflow;
+  unsigned char overflow[3];
+};
+
+} // namespace olb
+
+#endif
diff --git a/src/io/base64.hh b/src/io/base64.hh
new file mode 100644
index 0000000..7091fe7
--- /dev/null
+++ b/src/io/base64.hh
@@ -0,0 +1,200 @@
+/*  This file is part of the OpenLB library
+ *
+ *  Copyright (C) 2007 Jonas Latt
+ *  E-mail contact: info@openlb.net
+ *  The most recent release of OpenLB can be downloaded at
+ *  <http://www.openlb.net/>
+ *
+ *  This program is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License
+ *  as published by the Free Software Foundation; either version 2
+ *  of the License, or (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public
+ *  License along with this program; if not, write to the Free
+ *  Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+ *  Boston, MA  02110-1301, USA.
+*/
+
+/* Acknowledgment: The strategy adopted here to encode
+ * and decode Base64, and in particular the expression of the
+ * arrays Base64Encoder::enc64 and Base64Decoder::dec64,
+ * is inspired by the open source library b64 by Bob Trower,
+ * which is distributed with a MIT license at the address
+ * http://base64.sourceforge.net/b64.c
+ */
+
+#ifndef BASE64_HH
+#define BASE64_HH
+
+#include "base64.h"
+#include "core/olbDebug.h"
+#include <ostream>
+#include <istream>
+
+
+namespace olb {
+
+////////////// class Base64Encoder ////////////////////////////////////////////
+
+template<typename T>
+const char Base64Encoder<T>::enc64[65]=
+  "ABCDEFGHIJKLMNOPQRSTUVWXYZ" \
+  "abcdefghijklmnopqrstuvwxyz0123456789+/";
+
+template<typename T>
+Base64Encoder<T>::Base64Encoder(std::ostream& ostr_, size_t fullLength_)
+  : ostr(ostr_),
+    charFullLength(fullLength_ * sizeof(T)),
+    numWritten(0),
+    numOverflow(0)
+{ }
+
+template<typename T>
+void Base64Encoder<T>::encode(const T* data, size_t length)
+{
+  const unsigned char* charData = reinterpret_cast<const unsigned char*>(data);
+  size_t charLength = length * sizeof(T);
+  OLB_PRECONDITION( numWritten+charLength <= charFullLength );
+
+  size_t pos=0;
+  fillOverflow(charData, charLength, pos);
+  while (pos+3 <= charLength) {
+    encodeBlock(charData+pos);
+    pos += 3;
+  }
+  fillOverflow(charData, charLength, pos);
+  numWritten += charLength;
+  if (numWritten == charFullLength) {
+    flushOverflow();
+  }
+}
+
+template<typename T>
+void Base64Encoder<T>::fillOverflow(const unsigned char* charData, size_t charLength, size_t& pos)
+{
+  while (numOverflow < 3 && pos < charLength) {
+    overflow[numOverflow] = charData[pos];
+    ++numOverflow;
+    ++pos;
+  }
+  if (numOverflow == 3) {
+    encodeBlock(overflow);
+    numOverflow = 0;
+  }
+}
+
+template<typename T>
+void Base64Encoder<T>::flushOverflow()
+{
+  if (numOverflow > 0) {
+    for (int iOverflow = numOverflow; iOverflow<3; ++iOverflow) {
+      overflow[iOverflow] = 0;
+    }
+    encodeUnfinishedBlock(overflow, numOverflow);
+    numOverflow = 0;
+  }
+}
+
+template<typename T>
+void Base64Encoder<T>::encodeBlock( const unsigned char* data)
+{
+  ostr << enc64[ data[0] >> 2 ];
+  ostr << enc64[ ((data[0] & 0x03) << 4) | ((data[1] & 0xf0) >> 4) ];
+  ostr << (unsigned char) (enc64[ ((data[1] & 0x0f) << 2) | ((data[2] & 0xc0) >> 6) ]);
+  ostr << (unsigned char) (enc64[ data[2] & 0x3f ]);
+}
+
+template<typename T>
+void Base64Encoder<T>::encodeUnfinishedBlock( const unsigned char* data, int length )
+{
+  ostr << enc64[ data[0] >> 2 ];
+  ostr << enc64[ ((data[0] & 0x03) << 4) | ((data[1] & 0xf0) >> 4) ];
+  ostr << (unsigned char) (
+         length == 2 ?
+         enc64[ ((data[1] & 0x0f) << 2) | ((data[2] & 0xc0) >> 6) ] :
+         '='
+       );
+  ostr << (unsigned char) ( '=' );
+}
+
+
+////////////// struct Base64Decoder ////////////////////////////////////////////
+
+template<typename T>
+const char Base64Decoder<T>::dec64[82]=
+  "|###}rstuvwxyz{#######>?@"\
+  "ABCDEFGHIJKLMNOPQRSTUVW######XYZ"\
+  "[\\]^_`abcdefghijklmnopq";
+
+
+template<typename T>
+Base64Decoder<T>::Base64Decoder(std::istream& istr_, size_t fullLength_)
+  : istr(istr_),
+    charFullLength(fullLength_ * sizeof(T)),
+    numRead(0),
+    posOverflow(3)
+{ }
+
+template<typename T>
+void Base64Decoder<T>::decode(T* data, size_t length)
+{
+  unsigned char* charData = reinterpret_cast<unsigned char*>(data);
+  size_t charLength = length * sizeof(T);
+  OLB_PRECONDITION( numRead+charLength <= charFullLength );
+
+  size_t pos = 0;
+  flushOverflow(charData, charLength, pos);
+  while (pos+3 <= charLength) {
+    decodeBlock(charData+pos);
+    pos += 3;
+  }
+  if (pos < charLength) {
+    decodeBlock(overflow);
+    posOverflow=0;
+    flushOverflow(charData, charLength, pos);
+  }
+  numRead += charLength;
+}
+
+template<typename T>
+void Base64Decoder<T>::flushOverflow(unsigned char* charData, size_t charLength, size_t& pos)
+{
+  while (posOverflow < 3 && pos < charLength) {
+    charData[pos] = overflow[posOverflow];
+    ++pos;
+    ++posOverflow;
+  }
+}
+
+template<typename T>
+unsigned char Base64Decoder<T>::getNext()
+{
+  unsigned char nextChar;
+  istr >> nextChar;
+  return (unsigned char) (dec64[nextChar - 43] - 62);
+}
+
+template<typename T>
+void Base64Decoder<T>::decodeBlock(unsigned char* data)
+{
+  unsigned char input[4];
+  input[0] = getNext();
+  input[1] = getNext();
+  input[2] = getNext();
+  input[3] = getNext();
+  data[0] = (unsigned char) (input[0] << 2 | input[1] >> 4);
+  data[1] = (unsigned char) (input[1] << 4 | input[2] >> 2);
+  data[2] = (unsigned char) (((input[2] << 6) & 0xc0) | input[3]);
+}
+
+}  // namespace olb
+
+#endif
+
+
diff --git a/src/io/blockGifWriter.cpp b/src/io/blockGifWriter.cpp
new file mode 100644
index 0000000..087e07f
--- /dev/null
+++ b/src/io/blockGifWriter.cpp
@@ -0,0 +1,32 @@
+/*  This file is part of the OpenLB library
+ *
+ *  Copyright (C) 2015 Albert Mink, Mathias Krause
+ *  E-mail contact: info@openlb.net
+ *  The most recent release of OpenLB can be downloaded at
+ *  <http://www.openlb.net/>
+ *
+ *  This program is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License
+ *  as published by the Free Software Foundation; either version 2
+ *  of the License, or (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public
+ *  License along with this program; if not, write to the Free
+ *  Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+ *  Boston, MA  02110-1301, USA.
+*/
+
+#include "blockGifWriter.h"
+#include "blockGifWriter.hh"
+
+
+namespace olb {
+
+template class BlockGifWriter<double>;
+
+} // end namespace olb
diff --git a/src/io/blockGifWriter.h b/src/io/blockGifWriter.h
new file mode 100644
index 0000000..33923dc
--- /dev/null
+++ b/src/io/blockGifWriter.h
@@ -0,0 +1,90 @@
+/*  This file is part of the OpenLB library
+ *
+ *  Copyright (C) 2015 Albert Mink, Mathias J. Krause
+ *  E-mail contact: info@openlb.net
+ *  The most recent release of OpenLB can be downloaded at
+ *  <http://www.openlb.net/>
+ *
+ *  This program is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License
+ *  as published by the Free Software Foundation; either version 2
+ *  of the License, or (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public
+ *  License along with this program; if not, write to the Free
+ *  Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+ *  Boston, MA  02110-1301, USA.
+*/
+
+#ifndef BLOCK_GIF_WRITER_H
+#define BLOCK_GIF_WRITER_H
+
+#include <iomanip>
+#include "io/colormaps.h"
+#include "io/ostreamManager.h"
+#include "functors/lattice/blockBaseF2D.h"
+
+
+namespace olb {
+
+/** BlockGifWriter writes given functor data to image file of format .ppm
+ *
+ *  There are two different modes
+ *  1. mode: image maxValue and minValue are computed every time.
+ *           this implies that image data is scaled every time exactly to
+ *           interval [0,1]. this may lead to different scaling of the functor data
+ *           concerning the time steps
+ *  2. mode: image maxValue and minValue are passed by the user once.
+ *           this static use, prevents a rescaling effect for each time step.
+ *
+ *  \param map determines the color of the graphics
+ */
+template< typename T >
+class BlockGifWriter {
+public:
+  // constructor
+  BlockGifWriter( std::string const& map="leeloo" );
+
+  /** writes functor values normed to interval [0,1].
+   *  imageValue is computed according to :
+   *  if functorValue >= maxValue then the imageValue is clipped to 1
+   *  else imageValue = (minValue - functorValue) / (minValue - maxValue)
+   */
+  void write( BlockF2D<T>& f, T minValue, T maxValue, int iT=0,
+              std::string const& name="emptyName" );
+  /// writes functor data and determines its min-/maxValue
+  void write( BlockF2D<T>& f, int iT=0, std::string const& name="emptyName" );
+  ///  writes functors stored at pointerVec
+  void write(int iT=0);
+  ///  put functor to _pointerVec, to simplify writing process of several functors
+  void addFunctor( BlockF2D<T>& f, std::string const& name="emptyName" );
+  void addFunctor( BlockF2D<T>& f, T minValue, T maxValue, std::string const& name="emptyName" );
+
+private:
+  //  void ppm2gif(const std::string& fullNamePpm, const std::string& fullNameGif);
+  mutable OstreamManager clout;
+  int _colorRange;    // set to 1024
+  int _numColors;     // set to 1024
+  graphics::ColorMap<T> _colorMap;
+
+  /// Holds added functor, to simplify the use of write function
+  std::vector< BlockF2D<T>* > _pointerVec;
+  /// Holds the names of added functors
+  std::vector<std::string> _name;
+  /// Holds the scale instruction of added functors
+  std::vector<bool> _autoScale;
+  /// Holds the minValues of added functors
+  std::vector<T> _minValue;
+  /// Holds the maxValues of added functors
+  std::vector<T> _maxValue;
+};
+
+
+}  // namespace olb
+
+#endif
diff --git a/src/io/blockGifWriter.hh b/src/io/blockGifWriter.hh
new file mode 100644
index 0000000..ef95d6c
--- /dev/null
+++ b/src/io/blockGifWriter.hh
@@ -0,0 +1,202 @@
+/*  This file is part of the OpenLB library
+ *
+ *  Copyright (C) 2015 Albert Mink, Mathias Krause
+ *  E-mail contact: info@openlb.net
+ *  The most recent release of OpenLB can be downloaded at
+ *  <http://www.openlb.net/>
+ *
+ *  This program is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License
+ *  as published by the Free Software Foundation; either version 2
+ *  of the License, or (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public
+ *  License along with this program; if not, write to the Free
+ *  Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+ *  Boston, MA  02110-1301, USA.
+*/
+
+#ifndef BLOCK_GIF_WRITER_HH
+#define BLOCK_GIF_WRITER_HH
+
+#include <fstream>
+#include <string>
+#include <vector>
+
+#include "io/blockGifWriter.h"
+#include "io/fileName.h"
+#include "utilities/vectorHelpers.h"
+#include "core/singleton.h"
+#include "communication/mpiManager.h"
+
+namespace olb {
+
+
+template< typename T >
+BlockGifWriter<T>::BlockGifWriter(std::string const& map)
+  : clout(std::cout, "BlockGifWriter"), _colorRange(1024), _numColors(1024),
+    _colorMap(graphics::mapGenerators::generateMap<T>(map)), _minValue(0),
+    _maxValue(1)
+{ }
+
+template< typename T >
+void BlockGifWriter<T>::write(BlockF2D<T>& f, T minValue, T maxValue, int iT,
+                              std::string const& name)
+{
+  // [!] exeption image(f) != 1
+  if ( f.getTargetDim() != 1 ) {
+    clout << "Error: Functor targetDim is not 1. " << std::endl;
+    exit(-1);
+  } else {
+    if ( singleton::mpi().getRank() == 0 ) {
+      std::string fullNamePpm;
+      if ( name == "emptyName") {
+        fullNamePpm = createFileName( singleton::directories().getImageOutDir(),
+                                      f.getName(), iT);
+      } else {
+        fullNamePpm = createFileName( singleton::directories().getImageOutDir(),
+                                      name, iT);
+      }
+      fullNamePpm = fullNamePpm  + ".ppm" ;
+      std::ofstream fout( fullNamePpm.c